Data toggles

This box contains three toggles that control certain aspects of the fit. The first two are only relevant in a multiple data set fit. When setting up a project containing a multiple data set fit, it is sometimes useful to exclude an entire data set from the fit without deleting it from the project. This can be done with the first toggle. When a data set is excluded, it and all items beneath it are shown in brown text in the Data and Paths List to indicate that they have been excluded from the fit.

After the fit is complete, Artemis wants to show off her handiwork and display a plot of the data and the just-finished fit. In the case of a multiple data set fit, you might have a preference about which data set gets plotting. Click this toggle on for your prefered data set.

The third toggle tells Artemis to do a corefinement of the background spline when it performs the fit. This corefinement is, effectively, the same operation that was performed by Athena to remove the background from the data. The "rmin" parameter serves the same purpose as Athena's "rbkg" parameter. When the fit is performed with the background corefinement, a spline is used to fit the Fourier components of the data below "rmin" and the Feff paths are used to fit the Fourier components between "rmin" and "rmax". The number of parameters used to determine the spline is the number of independent points in that portion of the data: "2*delta_k*delta_R/pi", where "delta_k" is the range of the Fourier transform and "delta_R" is the range between 0 and "rmin". The advantage of doing the background corefinement, other than the possibility of making the fit look nicer at low R, is that correlations between the background parameters and the fitting parameters can be measured.

Fourier transform and fitting parameters

This box contains the controls used to set the ranges of the forward Fourier transform and of the fit. The fit range is also used as the backward Fourier transform range when a plot is q space is made. See "Pluck buttons" for a discussion of the little quare buttons marked with a blue x.

Other controls are used to set the functional forms of the Fourier transform window used in k and R. The widths of the sills of those functions are set usng the entry boxes labeled "dk" and "dr".

k-weight parameters

The controls in this box are used to set the values of k-weight to be used in the fits. There are togles for turning on k-weight of 1, 2, or 3. There is also a toggle for specifying an arbitrary value of k-weight.

These are the k-weight values used in the fit but not the k-weight used to plot the data. These two purposes of k-weight are handled independently by Artemis. See Plotting in Artemis for a discussion of the plotting k-weight controls.

People sometimes get confused by the concept of multipl k-weights for fitting. The prupose of choosing a low or high value for k-weight is to attempt to emphasize either the low- or high-k end of the data. Because different regions of the data are sensitive to different kinds of parameters, one might choose a low or high value to increase the precision of measurement of certain parameters. Doing multiple k-weight fits is a sort of compromise -- a way of emphasizing both ends of the data in the fit.

The fit is determined by minimizing a quantity called chi-square. Chi-square is evaluated by summing the squares of the difference between the data and the theory. Since the FT is complex, there is a real part and an imaginary part. So chi-square is proporitional to:

         /                                                    \
    sum <   Re[ data(R) - th(R) ]^2 + Im[ data(R) - th(R)]^2   >
     R   \                                                    /

In a multiple k-weight fit, there are simply more terms in the sum. Let's take a kw=1&3 fit as an example. This summation is made for the kw=1 data and theory. And the summation is made for the kw=3 data and theory. The summations are added together and the full sum is used to evaluate chi-square.

At the end of the day, there is only one set of guess parameters that have been optimized by the fit. These guess parameters along with the set parameters are used to evaluate the def parameters and the path parameters. The path parameters are used to evaluate the exafs equation for each path. The exafs equations for the paths are summed up to make the best-fit theoretical chi(k). You have a data chi(k) and a best-fit chi(k). Those can then be plotted however you like -- even using a k-weight that was not used in determining the fit.

Other parameters

The last box contains several controls that did not fit into theother boxes. There is a menu for selecting the fitting space. You can choose to fit the data in any of k, R, or q space. The default is to fit in R.

Epsilon is the uncertainty used to evaluate chi-square. Normally it is fine to let Artemis use the default value (which is determined from the RMS value of the data between 15 and 25 angstroms in R-space). In some situations, you may find it useful to explicitly set a value for epsilon.

After the fit, Artemis writes a log file documenting the fit. Among the information in that log file are the correlations between all the fitting parameters. You can set the level below which Artemis will exclude a correlation from this report.

Finally, there is a menu for selecting the path to use for phase corrected plots. This menu contains the first five paths from each Feff calculation used with the data set. When a path is selected for phase corrected plots, the full phase shift of that path -- both the central atom and scattering atom portions -- will be subtracted from anything that is Fourier transformed before it is plotted. If a path is selected for phase correction and you make a plot of, say, the data, the fit, and several paths, the selected phase shift will be subtracted from each item before it is plotted. Phase correction is for plotting only. Fits are always done on non-phase-corrected data.

Pluck buttons

Several of the controls on this page a have a small button with a blue x next to them. These are called pluck buttons and are used for grabbing values from the plot window. When you click on one of these buttons, a prompt will be written to echo area asking you to click on a pointin the plot. When you do so, the value that you clicked on will be inserted into the entry box adjacent to the pluck button. Artemis is careful not to let you pluck a k-value from a plot in R, or vice versa.

Context menus

As you pass the mouse over labels on the data page, the text under the mouse will change color. This color change is an indication that mouse clicks will do something. A left mouse click on one of these labels will cause a brief description of that parameter to be displayed in the echo area. Many of these descriptions also suggest reasonable values for the parameter.

Clicking the right mouse button on one of the labels will post a context menu of useful function. One such function is restore that parameter to its default value. If you have a muliple data set fit, the other menu options allow you to constrain the parameter between data sets.

The labels at the top of the boxes are all sensitive to the left mouse button. The labels atop the Fourier transform and fit range box and the k-weights box are also sensitive to the right mouse click.

The parameter listbox

This area contains a four-column list of all the parameters defined in a project. The left-most column counts the parameters. The second column contains a tag identifying the type of the parameter. The third column contains the parameter name. The right-most column contains the parameter's math expression.

Parameters are coded by color and by the tag in the second column. Guess parameters are written in purple text and have the "g:" tag. Def parameters are written in green text and have the "d:" tag. Set parameters are written in black text and have the "s:" tag. Restraints are written in pink text and have the "r:" tag. Skip parameters are written in grey text and have no tag. After parameters are written in blue-grey text and have the "a:" tag.

There are a large number of mouse clicks and key sequences that serve a purpose in the listbox:

1.

A left mouse click selects a parameter and displays it in the edit area.

2.

A double click of the left mouse button selects a parameter, displays it in the edit area, and prompts you for the parameter annotation. See "Parameter annotations".

3.

A right mouse click selects a parameter, displays it in the edit area, and posts a contextual menu about that parameter. The menu has several items in it. The "Move" submenu is sued to reposition the current parameter in the list. The "Make" submenu serves to change the type of the parameter. The "Copy" item will replicate the anchored parameter, appending a few characters to the end of its name. The "Build restraint" item is discussed below. The "Annotate" menu item prompts for the parameter annotation. The "Find" menu item will search through all parameter and path parameter math expressions and show you how that parameter is used in the project. The "Grab" menu item is only enabled for guess parameters and will insert the best-fit value from a fit as the value for that parameter. Finally the "Discard" menu item will remove that parameter from the list after prompting for confirmation.

4.

Control-d will define the parameter in the edit area.

5.

Control-g will grab the current parameters best-fit value from a fit.

6.

Control-e will show the editing area if it is hidden.

7.

Control-k and control-j will move the selection up and down in the list. Note that these two key-sequences serve to move the anchor up and down in the Data and Path List when the Guess, Def, Set page is not showing.

8.

Control-n will clear the selection and focus on the parameter name entry box so that you can create a new parameter.

9.

Control-y will prompt you to then hit any of the g, d, s, r, k or e keys to set the type of the parameter. This is only way of setting the parameter type that does not involve the mouse.

Extended selection

Multiple items in the list of parameters can be selected using the control-click, shift-click, and click-drag sequences described for the Data and Paths List and for the log viewer. Only the anchored list item (i.e. the one surreounded by a dashed line and displayed in the edit area) can have its name and math expression edited.

The advantage of extended selection is that certain of the context menu options discussed above in item #3 can operate on many parameters at once. By doing extended selection then clicking the right mouse button somewhere in the selected region, the context menu will be posted with options for the group of selected parameters. Currently, groups of parameters can have their types set and can be discarded in this manner.

If you right-click outside the selected region, the extended selection will be cleared and the parameter clicked on will be anchored and selected.

The edit area

There are three rows of controls in the edit area. The top row has two entry boxes. The smaller one on the left is for entering the name of the parameter. The larger one on the right is for entering the parameter's math expression.

Below the entry boxes are a set of five radiobuttons for selecting the type of parameter being edited.

At the bottom of the edit area are five buttons for acting upon the parameter being edited. The "Undo edit" button clears the entry boxes and discards whatever changes were just made. The "New" button is used to define a brand new parameter. It clears the entry boxes, unselects parameters in the listbox, and gives focus to entry box for entering the parameter name. The "Grab" button becomes enabled after a fit is run. It inserts the best-fit value for a guess parameter. The "Discard" button deletes a parameter from the list. A dialog pops up confirming deletion. Finally, the "Hide" button removes the edit area from view to allow more parameters to be visible in the listbox. When the edit area is hidden, it is replaced by a button for restoring the edit area.

Here are the details of the behavior of these controls:

1.

Hitting return in the parameter name entry box defines the parameter, inserts or updates it in the listbox, and puts focus on the math expression entry box. If a math expression has not yet been defined, the parameter will be defined as 0.

2.

Hitting return in the math expression entry box defines the parameter, inserts or updates it in the listbox, and leaves focus on the math expression entry box.

3.

Clicking on any of the radiobuttons defines the the parameter, inserts or updates it in the listbox, and leaves the focus unchanged.

Parameter annotations

An annotation is a short text string that is associated with the parameter. This string is written to the echo area whenever the parameter is selected in the listbox on the Guess, Def, Set page. The purpose of he annotation is to write a little hint about the role played by the parameter in the fiting model. If a guess parameters has no annotation when a fit is run, its annotation will be generated automatically. The automatic annotation for a guess parameter is its best fit value +/- its error bar. The automatic annotation for a def, after, or restrain parameter is its evaluated value after the fit.

Building restraints

One of the items in the context menu displayed when right-clicking on a parameter is for building restraints based on guess or def parameters. This tool provides a dialog for constructing one particular type of restraint -- the type that coerces a parameter to stay within a boundries for its value. The dialog prompts for a minimum and maximum value and for a term called the "amplifier". The math expression constructed is this one:

    restrain  param_res = penalty(param, min, max) * amp

The penalty function evaluates to 0 when "param" is between "min" and "max", to "abs(min-param)" when "param" is less than "min", and to "abs(param-max)" when "param" is greater than "max". This is added in quadrature to reduced chi-square as the fit is evaluated.

The amplifier term determines the magnitude of the penalty. A large value for "amp" will force the fitted value of "param" not to stray too far outside its bounds. A small value will allow the fit more freedom to let "param" deviate from your initial guess.

See the Ifeffit FAQ, question 8.1 for more discussion of restraints, including discussion of other ways to set restraints that do not involve the "penalty()" function.

A cautionary note: restraints are not always appropriate. As an example, if a fit is returning a negative value for sigma^2, it may not be appropriate to apply a stiff restraint as a way of forcing that sigma^2 to be a value that you expect. Often, a negative sigma^2 is indicative of some other problem in the fitting model such as excessive structural disorder, a coordination number that is forced to be too small, the incorrect atomic species for a backscatterer, or some such. Using a restraint on sigma^2 in a case like this would not fix the problem. Quite the opposite, it might foster a false sense of accomplishment by "fixing" the sigma^2 "problem" without actually addressing the actual problem in the fitting model.

Highlighting

There is an option in the GDS menu for highlighting parameters. This prompts you for a text string. Any parameter names or math expressions that match that string will be marked with a green background. This is particularly useful for large parameter lists. The text string is interpreted as a perl regular expression and so any valid perl metacharacters can be used. (This includes regular expressions using "(?{ code })" and other similar constructions, a practice the author of Artemis does not recommend, but does not prevent.)

Importing and exporting text files

For large, complex fitting models, it may be convenient to edit the parameter list with a text editor or even to write a program which generates the parameters and writes them to a text file. In that case, it is convenient to be able to import and export a textual respresentation of the parameter list. These files are of a simple format. Any line like these:

   guess  a   5
   set    b   6
   def    c   a+b

can imported to and exported from the Guess, Def, Set page via the GDS menu. In an imported file, any line beginning with any of "guess", "def", "set", "restrain", "after", or "skip" will be imported as a parameter. The second word on the line will be taken as the parameter name and the remaining words on the line will be concatinated to form the math expression. On export lines will follow this format:

   type name = math_expression

Very little error checking is performed upon import to verify that the parameter is defined sensibly, so use this feature with caution.

The title box

At the top is a text box for entering title lines identifying the crystallographic data. These lines will be written to the "feff.inp" file and to the top of the Feff interpretation page. This is a good place to cite the literature reference or to provide other important information about the crystal.

Crystal parameters

To the left side of the page are entry boxes for entering space group, lattice constants, and lattice angles of the crystal. A space group must always be provided. Atoms is very flexible about how the space group symbol is entered. You can use the Hermann-Maguin or Scheonflies symbols or the index of the space group from the International Tables. The algorithm that interprets the symbol is insensitive to white space and capitalization -- "P m -3 m" and "PM-3M" are interpreted the same. For complete details about how the symbols are interpreted, see the Atoms docuemntation on Bruce's web site.

Lattice constants are entered in units of Angstroms, angles are entered as decimal numbers in degrees (and not in arc minutes -- i.e. 89 and a half degrees is entered as 89.5 rather than 89'30"). Many space groups have symmetries that make some lattice angles and constants the same. In those situations, it is only necesary to fill in the essential values. For instance, a cubic space group only requires a value for the "a" constant. Atoms will know to set the other lattice constants the same and to set the angles to 90 degrees. For lower symmetry groups, you must provide all the necessary information.

Below the lattice constants are entry boxes for "Rmax" and the shift vector and a menu for selecting the absorption edge of the Feff calculation. "Rmax" is the radial extent of the cluster that will be written to the "feff.inp" file. Some space groups are given in the International Tables with two different origins -- i.e. the origin is placed at sites with two different point symmetries. The fractional coordinates of the sites are different for the two different settings of the crystal. In those cases, Atoms requires that you use a particular one of the two choices. If your input data has used the other origin choice, it should be fairly obvious. In that case, coordination numbers and distances to the coordination shells will usually be obviously wrong. When you use one of the space groups for which two origin choices exist, Artemis will issue a warning. If you suspect that the wrong origin choice has been used, insert the values for the shift vector that were reported in the warning message.

On occassion, crystals are reported in the literature using origins other than the standard one used in the International Tables. A famous example is germanium oxide. Here is the crystal data for GeO2:

   title GeO2 (hexagonal)
   space p 32 2 1
   a=4.98502       c=5.64800
   rmax=6.0        core=Ge
   shift   0 0 0.66667
   atoms
     Ge    0.4513  0.0     0.0
     O     0.3969  0.3021  0.0909

For some reason, the crystallography reference for this material uses an origin that is shifted by 2/3 in the z direction relative to the origin used in the International Tables. To get Atoms to compute this structure correctly, the shift vector given above must be used.

The atoms list

To the right side of the page is the list of unique crystallographic sites. As new sites are created, they are inserted into the list. The sites are not edited directly, instead the editing area at the bottom of the screen is used and the list of all sites is displayed here. This works much the same as the Guess, Def, Set page.

To edit a site, left-click on its entry in the list. It's element symbols, coordinates, and site tag will be displayed in the edit area. A right click on a site in the list will post a context menu with several functions that can be perfromed on that site. You can re-order the list using the "Move" menu item. A site can be copied and the copy added to the list using the "Copy" menu item. The "Discard" menu item completely removes the site from the list. The list supports extended selection. When many sites are selected (i.e. highlighted in yellow), the "Discard" menu item will work on all the selected sites.

Sites can also be reordered using the keyboard. "Alt-k" and "Alt-j" can be used to move the selected site up or down in the list.

The edit area

At the bottom of the page is the collection of widgets used to actually create and edit unique crystallographic sites. The element box is used to insert the two-letter element symbol for the site. The site will not be created if this is not a valid symbol. The tag can be any 10-letter string used to identify the site. The tag is used to differentiate sites that contain the same element.

The boxes for the "x", "y", and "z" coordinates can be filled with floating point numbers or simple fractions. That is, 0.5 and "1/2" are both acceptable. These coordinates are fractional positions in the unit cell and are not Cartesian coordinates.

Once you have created all sites in your crystal, click the "Run Atoms" button. This will process the crystallographic data, create the "feff.inp" file, display the "feff.inp" page.

Atoms template files

The "feff.inp" data that is generated when the "Run Atoms" button is pressed is determined by the contents of a special template file. Artemis is distributed with a number of template files serving different purposes. The structure of the "feff.inp" data is set by the value of the "atoms->template" preference. The default value is "feff", which tells Artemis to use the template file suitable for running Feff6.

If you want to run some other version of Feff, you should set the "atoms->template" preference variable to the appropriate value. Templates are provided with Artemis for writing Feff7 and Feff8 input files. Feff8 input files can be written which are suitable for XANES or non-self-consistent EXAFS calculations.

Sometimes, it is useful to modify template files for writing out specialized "feff.inp" data. If these modified template files are placed in "~/.horae/atp/" (unix) or "C:Program Files\Ifeffit\horae\atp" (windows), Artemis will be able to find them.

Final note

A full explanation of how the Atoms algorithms works is beyond the scope of this document page.

The interpretation chart

The colors and fonts used in the chart convey information:

Bold, black font

These are paths that have been imported into the project and are included in the fit.

Bold, brown font

These are paths that have been imported into the project but are excluded in the fit.

Normal, black text

These are paths that have not been imported into the project but which are available to be imported.

Normal, grey text

These are paths that are unavailable for importation into the project. These can be made available by re-running the Feff calculation. After the Feff run, it is best to choose the "import no paths" to avoid reimporting paths already in the project. After that, these paths will be written in normal, black text, indicating that they are available for import.

Light brown background

The light brown background is used to indicate single scattering paths.

Light blue background

The light blue background is used to indicate collinear or nearly collinear multiple scattering paths.

Context menus

There are interesting and useful context menus on every part of this page. These menus are available by right clicking.

Right clicking anywhere in the text box at the top of the page will pop up a menu with options for viewing files from the Feff calculation.

Right clicking in the interpretation chart will post a menu of options relevant to the path on the line on which you clicked. Each of the four kinds of paths given by the four fonts described above has its own menu.

For paths that are imported in the fit, the menu offers options for plotting the path, displaying that path's page, including or excluding the path in the fit, selecting or deselecting that path for plotting, making that path the default for evaluation of def parameters after a fit, displaying the text of the file containing the path, or discarding the path. The choices for including or excluding and for selecting or deselecting depend on the state of that path in the Data and Paths List. Also some options might be greyed out depending on the state of that path.

For paths that have not been imported into the project, the context menu allows you to import the path with the option of displaying its page or leaving the display on the Feff interpretation. For paths that are unavailable for import, a message saying so is posted when one of those lines is right-clicked.

The interpretation chart allows for extended selection of lines in the chart. You can select additional paths by holding the control key while clicking with the left mouse button. Holding the shift key while left clicking selects all line between the anchor (the one outlined with a dashed line) and the one you click on. You can also click and drag to select all the lines you drag over. When more than one line is selected, the content of the context menu change to reflect functionality that makes sense for many paths. Extended selection in the interpretation chart is therefore a good way of including/excluding, selecting/deselecting, or plotting a large number of paths.

The context menu that pops up when many lines are selected may be a little surprising. Its contents depend upon the state of the anchored line, which in this case is the one that you right-click on to post the menu. The options in the context menu will be suitable to the state of the anchored selection regardless of the states of the other selected lines. If you choose a menu item that does not make sense for some of the selected lines, those lines will be ignored.

Here is a concrete example. Suppose that you select a number of lines, some of which are included in the fit and some of which have not been imported in the fit. If you then right click on one of the included paths, you will get options appropriate to included paths. If you then ask to plot the selected paths along with the data, the included paths will be plotted and the imported paths will be ignored. If, instead, you click on one of the paths that has not been imported yet, the context menu will give you the option of importing the selected paths. In that case, the paths that have already been imported will be ignored.

Trouble shooting

On occassion you might see that lines in the Feff interpretation do not properly report on the contents of the path. When this happens, site tags are replaced by this string: "<?>". There are a couple common reasons you might see the "<?>" tags:

1.

You have done some advanced voodoo with Feff, editing the "files.dat" or "paths.dat" files then rerunning the last module to produce specialized output.

2.

You have discovered a bug in the algorithm Artemis uses to harvest information from the Feff calculation. IN that case, you should send the "feff.inp" file or the Artemis project file to Bruce so he can fix the problem.

Note that the appearance of the "<?>" tags is probably not an indication that Feff has misbehaved. The Feff calculation has to run to completion and generate its normal output before this problem can manifest itself. The Feff calculation is almost certainly usable to analyze the data. The Feff interpretation page is Artemis's attempt to organize information about the Feff calculation in some user-friendly format. That this organizational effort failed is not necessarily an indication that Feff failed.

k-Weighting

Below the plot buttons are a set of radiobuttons for setting the k-weight to use in the plots. The k-weight chosen will be used to weight a plot in k-space or to weight data for Fourier transforming. The same k-weight is used for each selected item. The button marked "kw" needs some explanation. When this button is chosen, the k-weight to use in the plot will be determined from the data being plotted. If the arbitrary k-weight enabled for the data set,the value for the arbitrary k-weight will be used, other wise the smallest k-weight value enabled will be used. There are two reason to use the "kw" button. One is to plot using your arbitrary weight. The other is to make a plot of two or more data sets using a different k-weight for each data set.

Note that these k-weight controls are unrelated to the controls which set the k-weight used in the fit. K-weighting for fitting and plotting are controlled independently.

Selecting What Gets Plotted

Below the k-weight radiobuttons are menus for choosing which part of the complex functions chi(R) or chi(q) to plot. Plots involving multiple parts of the complex functions (e.g. real+envelope) are not currently possible.

Below these menus are three checkbuttons used for plotting the Fourier transform window, the background function, and the residual. If the window button is pressed, the appropriate window function will be plotted in any plot. The background and residual functions are only plotted if one of the selected items is a fit. The background will only be plotted if a background corefinement was made for that fit. If a fit is not among the selected items, the background and residual will not be plotted. Note that a plot with more than one selected fit may be quite confusing if the background or residual buttons are depressed since the background and residual will be plotted for each fit.

The ranges over which the plot will be made in the three spaces are controlled by the three sets of entry boxes.

Extra Plotting Features

The two additional tabs in the plotting panel contain the controls for the following utilities:

Indicators

Indicators are vertical bars that can be placed at user-chosen locations in k-, R-, or q-space. These indicators will get displayed every time a plot is made. The idea is that indicators are a guide to the eye, drawing attention to a place of interest as the data being plotted changes.

Indicators selected in either k- or q-space will be plotted in both k- and q-space, but not in R-space. Likewise, indicators selected in R-space will not be plotted in k- or q-space.

Several characteristics of the indicators, including the number, the linetype, and the color, can be set in the Plot section of the preferences dialog.

The indicators play well with each of the plotting options described below.

Stacking

Stacking refers to a vertical displacement the various traces. This is most useful for plotting the various path contributions in k-space, but is sometimes useful in other kinds of plots as well. Stacking requires three parameters which are set in the stacking notecard. The first control is series of radio buttons for choosing whether stacking happens in k-space, always, or never. If the k-space option is chosen, then q-space plots of the real or imaginary parts will also be stacked. (Basically, the "k-space" choice refers to any wiggly function of wavenumber.) The other two controls set the initial offset value and the increment between staces.

Inverting

Inverting is a useful tool for displaying the path contributions in "|chi(R)|" plots. When this is selected, the "|chi(R)|" from any paths included in the plot will be multiplied by -1 so that they stick down below the zero-axis. Hopefully this kind of plot help reduce clutter while still helping to show which paths contribut where. The radiobuttons on this notecard allow you choose between never inverting, inverting "|chi(R)|", or inverting both "|chi(R)|" and "|chi(q)|". The real and imaginary parts in R- or q-space are never inverted. chi(k) is also never inverted. Inverting is turned off whenever stacking is selected and would effect the current plot (i.e. you cannot stack and invert at the same time).

Data set offsets

This feat ure is useful for multiple data set plots. This is similar to stacking in that the parameter denotes a vertical offset for use i the plot. Each trace associated with a particular data set is plotted at the same lavel, but the data sets will be offset by the amount specified by this control. This provides a way of simultaneously visualizing all parts of a multiple data set fit. Negative values are recommended, with a negative offset, the traces will be plotted in the same order from top to bottom as in the plot legend.

Stacking is disabled when data set offsets are used. Inverting is used with data set offsets, although I think this results in confusing plots.

Palettes || Using the Data and Paths List || =head1 ARTEMIS: Editing Math Expressions

ARTEMIS - Editing math expressions

The math expression editing dialog is a way of setting path parameter math expressions for many paths at once. It works on a given path parameter, e.g. it sets e0 or sigma^2 for many paths but does not touch other path parameters. This dialog is available in two different context menus. If you right click on a path parameter label on the path page and selection "Edit for many paths", then the dialog will pop up for editing that parameter. If you right click on an entry on the Feff interpretation page and select the "Edit path parameters" cascade, then select a path parameter, the dialog will pop up for editing that parameter.

Operation of the dialog

The dialog is fairly simple. At the top is a text entry box for typing in your math expression. Below that are various radiobuttons for specifying how to apply the math expression to the various paths in your project. The options are:

1.

Add the math expression to every path in the current Feff calculation.

2.

Add the math expression to every path in the each Feff calculation.

3.

Add the math expression to every path in the each Feff calculation associated with the current data set.

4.

Add the math expression to selected paths (i.e. the ones highlighted in orange in the Data and Paths list).

Tokens

You can write your math expressions using token. Tokens are short character strings which will be replaced by path-specific information as the math expression is applied to each path. The tokens are:

%i

The path index from the Feff calculation. This is actually computed from the name of the `feffNNNN.dat' file from the Feff calculation. For instance, if the file is `feff0029.dat', then %i will expand to 29.

%I

The path index from the Feff calculation, padded to fill four characters. For instance, if the file is `feff0029.dat', then %I will expand to 0029.

%r

The effective path length (or "reff") from the Feff calculation for the path.

%d

The degeneracy of the path.

%D

A template for the Debye function. This always expands to the string "debye(temp,thetad)" and may need be edited after the fact to use the correct variable names. This is offered because the author finds it hard to remember the order of the arguments to the Debye function.

%E

A template for the Einstein function. This always expands to the string "eins(temp,thetae)" and may need be edited after the fact to use the correct variable names. This is offered because the author finds it hard to remember the order of the arguments to the Einstein function.